LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 3d metal shear simulation

units		metal
boundary	s s p

atom_style	atomic
lattice		fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region		box block 0 16.0 0 10.0 0 2.828427
create_box	3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
  1 by 1 by 1 MPI processor grid

lattice		fcc 3.52 orient	x 1 0 0 orient y 0 1 1 orient z 0 -1 1 		origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms	1 box
Created 1912 atoms
  Time spent = 0.000714779 secs

pair_style	eam
pair_coeff	* * Ni_u3.eam
Reading potential file Ni_u3.eam with DATE: 2007-06-11

neighbor	0.3 bin
neigh_modify	delay 5

region		lower block INF INF INF 0.9 INF INF
region		upper block INF INF 6.1 INF INF INF
group		lower region lower
264 atoms in group lower
group		upper region upper
264 atoms in group upper
group		boundary union lower upper
528 atoms in group boundary
group		mobile subtract all boundary
1384 atoms in group mobile

set		group lower type 2
  264 settings made for type
set		group upper type 3
  264 settings made for type

# void

region		void cylinder z 8 3.535534 2.5 INF INF
delete_atoms	region void
Deleted 204 atoms, new total = 1708

# temp controllers

compute		new3d mobile temp
compute		new2d mobile temp/partial 0 1 1

# equilibrate

velocity	mobile create 300.0 5812775 temp new3d
fix		1 all nve
fix		2 boundary setforce 0.0 0.0 0.0

fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify	3 temp new3d

thermo		25
thermo_modify	temp new3d
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

timestep	0.001
run		100
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.1
  ghost atom cutoff = 5.1
  binsize = 2.55, bins = 23 14 4
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair eam, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.469 | 3.469 | 3.469 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0          300   -7358.6159            0   -7312.8966   -9600.8353     19547.02 
      25    222.66197   -7321.4403            0   -7287.5071    562.28854     19547.02 
      50          300   -7292.2273            0    -7246.508    7555.5059    19688.542 
      75    292.67603   -7286.2016            0   -7241.5984     6825.409    19746.217 
     100          300   -7297.4174            0    -7251.698    1627.2455    19775.648 
Loop time of 0.248797 on 1 procs for 100 steps with 1708 atoms

Performance: 34.727 ns/day, 0.691 hours/ns, 401.933 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.2343     | 0.2343     | 0.2343     |   0.0 | 94.17
Neigh   | 0.0084395  | 0.0084395  | 0.0084395  |   0.0 |  3.39
Comm    | 0.0016763  | 0.0016763  | 0.0016763  |   0.0 |  0.67
Output  | 0.0001018  | 0.0001018  | 0.0001018  |   0.0 |  0.04
Modify  | 0.0030863  | 0.0030863  | 0.0030863  |   0.0 |  1.24
Other   |            | 0.001193   |            |       |  0.48

Nlocal:    1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    1898 ave 1898 max 1898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    39444 ave 39444 max 39444 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 39444
Ave neighs/atom = 23.0937
Neighbor list builds = 4
Dangerous builds = 0

# shear

velocity	upper set 1.0 0 0
velocity	mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes

unfix		3
fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify	3 temp new2d

#dump		1 all atom 100 dump.shear.void

#dump		2 all image 100 image.*.jpg type type #		axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify	2 pad 4

#dump		3 all movie 100 movie.mpg type type #		axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify	3 pad 4

thermo		100
thermo_modify	temp new2d
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

reset_timestep	0
run		3000
Per MPI rank memory allocation (min/avg/max) = 3.469 | 3.469 | 3.469 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0    296.68961   -7297.4174            0   -7267.2741    785.80272    19779.424 
     100    290.29095   -7309.7136            0   -7280.2205   -5956.8739    19838.833 
     200     290.7321   -7306.4656            0   -7276.9277   -7416.8075    19927.094 
     300    293.23139   -7304.0943            0   -7274.3024   -11007.913    20043.774 
     400    293.81383   -7299.0837            0   -7269.2327   -7881.9544    20105.809 
     500    291.74006   -7299.9579            0   -7270.3176   -5632.3029    20145.528 
     600    303.46178   -7291.4986            0   -7260.6673   -1007.7166    20277.444 
     700          300     -7287.94            0   -7257.4605   -2202.5895    20399.422 
     800          300   -7280.4057            0   -7249.9261   -2873.4512    20520.809 
     900    292.91304   -7272.7185            0    -7242.959   -1775.2103    20641.435 
    1000    307.95389   -7265.1734            0   -7233.8857   -1238.3887    20758.693 
    1100    300.18687   -7260.1143            0   -7229.6158   -1847.3847    20889.388 
    1200     302.0476   -7255.9161            0   -7225.2285   -1891.5186    21012.754 
    1300          300   -7259.2628            0   -7228.7833   -3188.9692     21119.02 
    1400          300   -7265.4307            0   -7234.9511   -6111.2082    21252.157 
    1500    308.76375   -7271.0052            0   -7239.6352   -6108.8951    21369.416 
    1600          300   -7275.2316            0   -7244.7521   -8524.4552     21500.11 
    1700     309.2379   -7278.5657            0   -7247.1476    -13756.27     21618.59 
    1800          300   -7284.3098            0   -7253.8303   -14336.393     21728.52 
    1900    299.68683   -7283.3891            0   -7252.9413    -14440.43    21854.329 
    2000    297.67313    -7274.874            0   -7244.6309   -20446.625    21986.245 
    2100    304.15363   -7269.8329            0   -7238.9314   -19764.677    22101.061 
    2200    299.81061   -7269.2652            0   -7238.8049   -16585.297    22224.427 
    2300    299.34921   -7268.2843            0   -7237.8709   -15838.717     22345.35 
    2400     300.9448   -7259.5402            0   -7228.9646   -14597.506    22471.159 
    2500    297.43667   -7257.9882            0   -7227.7691   -17830.252    22589.639 
    2600          300   -7253.3202            0   -7222.8407   -18528.376     22717.89 
    2700    304.89923   -7253.0865            0   -7222.1092   -20198.406    22831.485 
    2800    293.40764   -7248.9658            0    -7219.156   -17298.989    22959.736 
    2900    306.87934   -7249.3942            0   -7218.2158   -17152.689    23078.216 
    3000    308.14535   -7244.6151            0    -7213.308   -15383.029    23210.132 
Loop time of 7.37965 on 1 procs for 3000 steps with 1708 atoms

Performance: 35.124 ns/day, 0.683 hours/ns, 406.523 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 6.7514     | 6.7514     | 6.7514     |   0.0 | 91.49
Neigh   | 0.45084    | 0.45084    | 0.45084    |   0.0 |  6.11
Comm    | 0.053905   | 0.053905   | 0.053905   |   0.0 |  0.73
Output  | 0.00081897 | 0.00081897 | 0.00081897 |   0.0 |  0.01
Modify  | 0.090654   | 0.090654   | 0.090654   |   0.0 |  1.23
Other   |            | 0.032      |            |       |  0.43

Nlocal:    1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    1875 ave 1875 max 1875 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    38660 ave 38660 max 38660 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 38660
Ave neighs/atom = 22.6347
Neighbor list builds = 209
Dangerous builds = 0
Total wall time: 0:00:07
